Integrated carbon nanotube field effect transistor and nanochannel for sequencing

ABSTRACT

A mechanism is provided for base recognition of an integrated transistor and nanochannel. A target molecule is forced down to a carbon nanotube a single base at a time in the nanochannel by applying a gate voltage to a top electrode, and/or a narrow thickness of the nanochannel. The nanochannel exposes an exposed portion of the carbon nanotube at a bottom wall, and the top electrode is positioned over the exposed portion. The exposed portion of the carbon nanotube is smaller than the distance between bases to only accommodate the single base at a time. The target molecule is stretched by the narrow thickness and by applying a traverse voltage across a length direction of the nanochannel. The target molecule is frictionally restricted by the narrow thickness of the nanochannel to stretch is restrictedly translocates in the length direction. Current is measured to determine an identity of the single base.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 13/690,963, entitled “INTEGRATED CARBON NANOTUBE FIELDTRANSISTOR AND NANOCHANNEL FOR SEQUENCING”, filed on Nov. 30, 2012,which is incorporated herein by reference in its entirety.

BACKGROUND

The present invention relates to nanodevices, and more specifically, tosequencing using an integrated carbon nanotube field effect transistorand nanochannel.

Nanopore sequencing is a method for determining the order in whichnucleotides occur on a strand of deoxyribonucleic acid (DNA). A nanopore(also referred to a pore, nanochannel, hole, etc.) can be a small holein the order of several nanometers in internal diameter. The theorybehind nanopore sequencing is about what occurs when the nanopore issubmerged in a conducting fluid and an electric potential (voltage) isapplied across the nanopore. Under these conditions, a slight electriccurrent due to conduction of ions through the nanopore can be measured,and the amount of current is very sensitive to the size and shape of thenanopore. If single bases or strands of DNA pass (or part of the DNAmolecule passes) through the nanopore, this can create a change in themagnitude of the current through the nanopore. Other electrical oroptical sensors can also be positioned around the nanopore so that DNAbases can be differentiated while the DNA passes through the nanopore.

The DNA can be driven through the nanopore by using various methods, sothat the DNA might eventually pass through the nanopore. The scale ofthe nanopore can have the effect that the DNA may be forced through thehole as a long string, one base at a time, like thread through the eyeof a needle. Recently, there has been growing interest in applyingnanopores as sensors for rapid analysis of biomolecules such asdeoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, etc.Special emphasis has been given to applications of nanopores for DNAsequencing, as this technology holds the promise to reduce the cost ofsequencing below $1000/human genome.

SUMMARY

According to an embodiment, a method for base recognition in anintegration of a transistor and a nanochannel is provided. The methodincludes forcing a target molecule down to a carbon nanotube a singlebase at a time in the nanochannel. The target molecule is forced to thecarbon nanotube by applying a gate voltage to a top electrode of thetransistor, by a narrow thickness of the nanochannel, or both byapplying the gate voltage to the top electrode of the transistor and bythe narrow thickness of the nanochannel. The nanochannel having beenpatterned over the carbon nanotube exposes an exposed portion of thecarbon nanotube at a bottom wall of the carbon nanotube, where the topelectrode of the transistor is positioned over the exposed portion ofthe carbon nanotube through the nanochannel. The exposed portion of thecarbon nanotube is smaller than a separating distance between bases onthe target molecule, and the exposed portion of the carbon nanotube isconfigured to only accommodate the single base at a time. The targetmolecule is stretched by the narrow thickness of the nanochannel and byapplying a traverse voltage across a length direction of the nanochannelbetween a first electrode and a second electrode at opposite ends of thenanochannel in the length direction. The target molecule is frictionallyrestricted by the narrow thickness of the nanochannel causing the targetmolecule to stretch as the target molecule restrictedly translocates inthe length direction while the traverse voltage is applied. The methodincludes measuring a transistor current while the single base of thetarget molecule is forced down to the exposed portion of the carbonnanotube in the nanochannel. The single base affects the transistorcurrent. The method includes determining an identity of the single baseaccording to a change in the transistor current while the single base isforced down to the exposed portion of the carbon nanotube in thenanochannel.

According to an embodiment, a system for base recognition of a targetmolecule is provided. The system includes a transistor having a sourceelectrode, a drain electrode, and a top electrode. The source electrodeis electrically connected to the drain electrode by a carbon nanotube. Ananochannel is formed perpendicularly to the carbon nanotube and formedwith a longitudinal direction extending away from the source electrodeand the drain electrode. The nanochannel is formed of an insulatinglayer except at a single bottom location of the nanochannel. The singlebottom location of the nanochannel is an exposed portion of the carbonnanotube, and the nanochannel is only formed of the carbon nanotube atthe single bottom location. A size of the exposed portion of the carbonnanotube at the single bottom location is less than a separationdistance between bases of the target molecule. The top electrode ispositioned above the nanochannel to vertically line up to the exposedportion of the carbon nanotube at the single bottom location. The topelectrode forces the target molecule down to the carbon nanotube asingle base at a time in the nanochannel, and the target molecule isforced to the carbon nanotube by applying a gate voltage to the topelectrode of the transistor and by a narrow thickness of thenanochannel. A transistor current is measured while the single base ofthe target molecule is forced down to the carbon nanotube in thenanochannel, so that the single base affects the transistor current. Anidentity of the single base is determined according to a change in thetransistor current while the single base is forced down to the exposedportion of the carbon nanotube in the nanochannel.

Additional features and advantages are realized through the techniquesof the present invention. Other embodiments and aspects of the inventionare described in detail herein and are considered a part of the claimedinvention. For a better understanding of the invention with theadvantages and the features, refer to the description and to thedrawings.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The subject matter which is regarded as the invention is particularlypointed out and distinctly claimed in the claims at the conclusion ofthe specification. The forgoing and other features, and advantages ofthe invention are apparent from the following detailed description takenin conjunction with the accompanying drawings in which:

FIGS. 1A through 1E illustrate cross-sectional views of fabricating anintegrated carbon nanotube field effect transistor (CNT-FET) andnanochannel device according to an embodiment, in which:

FIG. 1A is a cross-sectional view of the device with a carbon nanotube;

FIG. 1B is a cross-sectional view of an electrically insulating layerdeposited on the surface of the device;

FIG. 1C is a cross-sectional view of a nanochannel or nanotrench formedthrough the insulating layer exposing the carbon nanotube;

FIG. 1D is a cross-sectional view of another electrically insulatinglayer deposited on the previous insulating layer to seal thenanochannel; and

FIG. 1E is a cross-sectional view of the device with electrodesdeposited.

FIG. 2A is a cross-sectional view of an integrated carbon nanotube fieldeffect transistor and nanochannel system according to an embodiment.

FIG. 2B is a top view the integrated carbon nanotube field effecttransistor and nanochannel system according to an embodiment.

FIG. 3A is an abbreviated version of a cross-sectional view of thecarbon nanotube field effect transistor and nanochannel system accordingto an embodiment.

FIG. 3B is an abbreviated version of a top view of the carbon nanotubefield effect transistor and nanochannel system according to anembodiment.

FIGS. 4A and 4B together are a flow diagram illustrating a method forbase recognition in a transistor and a nanochannel system according toan embodiment.

FIG. 5 is a block diagram that illustrates an example of a computer(computer test setup) having capabilities, which may be included inand/or combined with embodiments.

DETAILED DESCRIPTION

An embodiment of the present invention provides techniques to integratethe carbon nanotube field effect transistor (CNT-FET) and nanochannelfor DNA/RNA sequencing. Single or double strand DNA/RNA can be pulledthrough the nanochannel which can confine the motion of DNA/RNA. TheCNT-FET can read the nucleotide (i.e., base) information when theDNA/RNA moves over the carbon nanotube inside nanochannel. The DNA/RNAcan be pulled down towards the carbon nanotube by a vertical electricalfield. The DNA/RNA also can be stretched by the transverse electricalfield and/or physical size of the interface between the carbon nanotubeand the top sealing insulating film.

Currently, different state of the art methods are employed to controlthe trap, ratchet the long DNA/RNA, and sense single nucleotideinformation. Those methods may have their own advantages, but have notrealized the DNA/RNA sequencing in low cost and short time with highaccuracy. The embodiment utilizes the CNT-FET as a sensor to read thenucleotide information when the DNA/RNA is moving over the carbonnanotube. The nanochannel, vertical electrical field, and transverseelectrical field can confine the conformation and movement of DNA/RNA inthe nanochannel.

FIGS. 1A through 1E illustrate cross-sectional views of fabricating theintegrated the carbon nanotube field effect transistor (CNT-FET) andnanochannel device 100 according to an embodiment. FIGS. 1A through 1Emay be generally referred to as FIG. 1. FIG. 1 illustrates the processesto integrate the CNT-FET and nanochannel for DNA/RNA sequencing so thatthe bases of a target molecule being tested can be individually pressedto an exposed portion of the carbon nanotube.

FIG. 1A is a cross-sectional view of forming the multilayered device100. The device 100 includes a substrate 101 which may be anyelectrically insulating substrate such as silicon. An electricallyinsulating film 102 is deposited on the substrate 101. The electricallyinsulating film 102 may be a dielectric material such as hafnium oxide.A carbon nanotube 103 is selectively placed on the surface of theelectrically insulating film 102.

FIG. 1B illustrates that an electrically insulating film 104 which maybe grown with atomic layer deposition to control the accuracy ofthickness. The insulating film may be silicon dioxide, aluminum oxide,etc. The thickness of the electrically insulating film 102 can be a fewto tens of nanometers, such as, e.g., 10 nm. The thickness of theelectrically insulating film 104 can be, e.g., 3 to 5 nm.

FIG. 1C illustrates a nanochannel 105 (e.g., a nanotrench) formedthrough the insulating film 104 down to the carbon nanotube 103. Thebottom of the nanochannel 105 is the carbon nanotube 103 (itself) at anisolated location that exposes the carbon nanotube 103 (as discussedfurther herein). The height of the nanochannel 105 is the thickness ofthe insulating film 104 deposited on the carbon nanotube 103. Forexample, the thickness of the insulating film 104 deposited on thecarbon nanotube 103 may be controlled to be 1 to 2 nanometers (nm), suchthat the depth/height of the nanochannel 105 is correspondingly 1 to 2nm. The nanochannel 105 may be fabricated by standard semiconductortechnology, such as, e.g., e-beam lithography, helium ion microscope,etc.

FIG. 1D illustrates an electrically insulating film 106 deposited on theinsulating film 104 to seal the nanochannel 105. The micro contactprinting (as film transfer) may be employed to fabricate theelectrically insulating film 106 as understood by one skilled one theart. As one example, the whole piece of electrically insulating film 106is first formed on other substrates, and then transferred onto thenanochannel 105. So electrically insulating film 106 is placed on thetop the nanochannel 105, bonding with the insulating film 104 andsealing nanochannel 105. Accordingly, the electrically insulating film106 does not fill the inside of the nanochannel 105.

The nanochannel 105 is formed with the carbon nanotube 103 as a bottomportion, the insulating film 104 as the nanochannel 105 sidewalls, andthe electrically insulating film 106 as the top of the nanochannel 105.The length of the nanochannel may be 100 nm to several micrometers inlength. In one case, the insulating film 106 may be deposited on theinsulating film 104 before the nanochannel 105 is formed. In this case,the nanochannel 105 is opened through the insulating film 104 after theinsulating film 106 has been deposited.

In FIG. 1E, electrodes 107 and 108 are respectively deposited onopposite sides of the carbon nanotube 103. The electrodes 107 and 108are contacts physically and electrically connected to the carbonnanotube 103. A top electrode 109 is deposited on the electricallyinsulating film 106. The electrodes 107 and 108 may be metal contactsfor the carbon nanotube 103, and the top electrode 109 may be a metalcontact (not connected to the carbon nanotube 103). The metal contactsof electrodes 107, 108, and 109 may be any metal such as gold, titaniumnitride, etc.

FIGS. 2A and 2B illustrate an integrated carbon nanotube field effecttransistor and nanochannel system 200 of the device 100 according to anembodiment. FIGS. 2A and 2B may generally be referred to as FIG. 2.

FIG. 2A is a cross-sectional view of the system 200. A voltage source215 is connected to the substrate 101 and connected to the top electrode109. The voltage source 215 produces a gate voltage bias for the CNT-FETdevice 100. The gate voltage bias of the voltage source 215 generatesthe vertical electrical field 205 between the substrate 101 and topelectrode 109, which correspondingly generates downward forces 210 thatpull the DNA or RNA inside the nanochannel 105 towards the carbonnanotube 103. The arrows for the vertical electrical field 205 and thedownward forces 207 are shown to the left of the figure so as not toobstruct the details, but it is understood that the vertical electricalfield 205 and the downward forces 207 are in the device 100. The ground216 is connected to the negative side of the voltage source 215 and topelectrode 109.

FIG. 2B is a top view of the system 200. Inlet 210 and outlet 209 arethe locations for an inlet reservoir (with the DNA/RNA molecules assamples to be sequenced) and an outlet reservoir to capture themolecules. The inlet and outlet reservoirs are not shown in FIG. 2 so atnot to obscure the figure but are understood by one skilled in the art.The inlet 210 and outlet 209 represent that the two reservoirs have beenlifted from the FIG. 2B so that the nanochannel 105 can be viewed. Theinlet and outlet reservoirs are respectively sealed at the inlet 210 andoutlet 209. The inlet and outlet reservoirs and the nanochannel 105 arefilled with a buffer solution. The buffer solution is an electricallyconductive electrolyte solution as understood by one skilled in the art.The DNA/RNA sample can be placed into the buffer solution (e.g.,introduced into the inlet reservoir) for sensing.

Electrodes 218 and 219 are electrodes that are connected to a voltagesource 211 and ammeter 212. The electrodes 218 and 219 may besilver/silver chloride, platinum, etc. DNA (as a target molecule 305shown in FIG. 3) will be pulled through the nanochannel 105 by theelectrical field generated by voltage of the voltage source 211. Theammeter 212 can monitor/measure the ionic current change through thenanochannel 105 when the DNA or RNA is captured and driven inside thenanochannel 105. The change (e.g., drop) in ionic current when thetarget molecule is in the nanochannel 105, lets the operator (orcomputer 500 in FIG. 5) know that the target molecule is present.

The positive side of a voltage source 213 may be connected to electrode107 (as the source) and the negative side of the voltage source 213 maybe connected to the electrode 108 (as the drain), voltage source 213produces the voltage for the CNT-FET device 100. Ammeter 214monitors/measures the source-drain current (i.e., transistor current)through the carbon nanotube 103 (e.g., from electrode 107 to electrode108) in the CNT-FET device 100 which can detect nucleotide information(based on the change in source-drain current (i.e., transistor current))when the DNA/RNA passes over (and touches) the carbon nanotube 103inside nanochannel 105. The negative voltage applied to the topelectrode 109 also pushes the negatively charged DNA molecule to thecarbon nanotube 103 for base sensing at a specific bottom location ofthe nanochannel 105 at which the carbon nanotube 103 is exposed.

When no target molecule is in the nanochannel 105, a baseline currentcurve (e.g., measured by ammeter 214) is established by a voltage sweepof the voltage source 213 (e.g., for voltages 1-5) to generate abaseline voltage versus current curve for the transistor. For example,the voltage of voltage source 213 is applied to the electrodes 107 and108 and the transistor current is measured by ammeter 214. From aconventional current flow, current flows from voltage source 213, intoelectrode 107, through the carbon nanotube 103 (e.g., through themetallic shell), out through the electrode 108, into ammeter 214 (fortransistor current measurement), and into the negative side of thevoltage source 213.

Also, a baseline (nucleotide) current is established for each base suchas base A, base G, base C, and base T for a DNA molecule by individuallyintroducing a (previously) known base into the system 200 for testing toobtain the transistor current unique to each base. As one example case,only base A is introduced into the inlet reservoir at inlet 210. Whenbase A is pulled into the nanochannel 105 by the voltage of voltagesource 211 (e.g., the force of the electric field and the force of thenegative polarity of the electrode 218 pushing the negatively chargedDNA molecule), the base A interacts with (e.g., touches) the carbonnanotube 103 at a specific bottom location 310 (hole/via) of thenanochannel 105 as shown in FIG. 3B. The charges on the base A (in thisexample) will cause a transfer of charges to the electrical currentcarriers flowing on the carbon nanotube 103. This will cause theelectrical current (measured by the ammeter 214) on the carbon nanotube103 to change (e.g., drop or increase) as the base A touches the carbonnanotube 103 at the specific bottom location 310 of the nanochannel 105.This process individually occurs for base A, G, C, and T to establish atransistor current baseline, and the respective electrical currentchange (e.g., the magnitude and time duration of the change) is measuredand recorded for each of the respective bases A, G, C, and T. Therespective transistor current change (e.g., drop in electrical currentfor a particular time duration) is used to compare against and identifybases on a target molecule that needs to be sequenced.

Once the system 200 is flushed (as understood by one skilled in theart), the target molecule 305 to be tested is introduced into the inletreservoir at the inlet 210. The voltage of voltage sources 211, 213, and215 are all turned on (and remain on during testing). By the voltage ofvoltage source 211 (i.e., electric voltage potential via electrodes 218and 219 in the respective inlet and outlet reservoirs), the electricfield (not shown) and negative polarity (of electrode 218 push)translocates (moves) the target molecule into (and through) thenanochannel 105. While in the nanochannel 105, the voltage of voltagesource 215 drives/pushes the target molecule (i.e., the backbone) and asingle base against (i.e., to touch) the carbon nanotube 103 at thespecific bottom location 310. While this single base is touching thecarbon nanotube 103 and while the voltage of voltage source 213 isapplied, the electrical current changes (i.e., source drain current ofthe transistor drops or increases for a time duration) while the singlebase touches the carbon nanotube 103 through the specific bottomlocation 310 of the nanochannel 105.

FIG. 3A illustrates an abbreviated version of a cross-sectional view ofthe system 200 with the carbon nanotube field effect transistor(CNT-FET) and nanochannel device 100. So as not to obscure FIGS. 3A and3B for the reader, certain elements of the system 200 are omitted but itis understood that the omitted elements are part of the figures asdiscussed herein. FIG. 3A illustrates how the voltage applied to the topelectrode 109 (e.g., gate electrode) drives the target molecule 305down, by particularly pressing a single base 350 to the carbon nanotube103 at the specific bottom location 310 of the nanochannel 105. Thecharges (positive or negative) on this particular base 350 interacts theelectrical current (charge carriers) flowing on the carbon nanotube 103,to cause the electrical current to change (drop or increase) whenmeasured by the ammeter 214. The electrical field 205 is shown pointingup (and to the left side of the figure so as not obstruct the figure).The downward forces 210 (including the negative voltage polarity appliedto the top electrode 109) are pushing the single base 350 on to (anexposed portion 315 of) carbon nanotube 103, while the other bases suchas bases 351 and 352 do not touch the carbon nanotube 103 in thenanochannel 105 (at the same time that the single base 350 touches thecarbon nanotube 103). The distance X separating each base of the targetmolecule 305 (such as DNA or RNA) is greater than “d” half of thediameter of the carbon nanotube 103. As such, this ensures that only asingle base of the target molecule 305 touches and interacts with thecarbon nanotube 103 at a time, because any two bases are too far apart.As an example, the distance X between the bases may be 0.7 nm while d(half of the diameter of the carbon nanotube) may be 0.5 nm.

Also, the thickness (also referred to as the depth and height) of thenanochannel 105 is narrow compared to the height and size of the basesof the target molecule 305. This narrow thickness provides two benefits.The narrowed thickness of the nanochannel 105 causes the bases (andbackbone of the target molecule 305) to frictionally rub the innersurface of the nanochannel 105 as the traverse electric field (of thevoltage source 212) advances the target molecule 305 through thenanochannel 105. This friction causes the target molecule 305 to stretchfor sequencing/reading. Also, the narrowed thickness of the nanochannel105 helps to confine the bases of the target molecule 305 so that thebases can touch (exposed portion of) the carbon nanotube 103 at thespecific bottom location 310 of the nanochannel 105. The diameter ofsingle-stranded DNA is about 1 nm. In order to physically stretch thesingle-stranded DNA 305, the thickness of the nanochannel 105 should bearound 2 nm. The gap is about 1 nm between the carbon nanotube 103 andthe top cover 106. So the single strand DNA can be stretched by thephysical size of nanochannel 105 when the single strand DNA 305 ispulled through the nanochannel 105 by the electrical field between twoelectrodes 218 and 219.

This process of reading the bases of the target molecule 305 occurs foreach of the bases, and the change in electrical current (i.e.,transistor current flowing over carbon nanotube 103) when eachindividual base touches the carbon nanotube 103 is respectively measured(by ammeter 214) and recorded for each base (e.g., by the computer 500).Accordingly, the change in electrical current (and time duration) isused to compare against (and match) the baseline change in electricalcurrent for each of the respective bases A, G, C, and T (measured at theonset). For example, the change in electrical current for the knownbases previously measured may have shown that the baseline currentamplitude of base A dropped to amplitude A at 2 volts, the baselinecurrent amplitude of base G dropped to amplitude G at 2 volts, thebaseline current amplitude of base C dropped to amplitude C at 2 volts,and the baseline current amplitude of base T dropped to amplitude T(e.g., at 2 volts applied by the voltage source 213). These baselineelectrical currents for the known bases are compared against theamplitude measured for the individual (unknown) bases of the targetmolecule 305 (e.g., at 2 volts applied by the voltage source 213).

FIG. 3B illustrates an abbreviated version of the system 200 from a topview. Particularly, top electrode 109 and the top sealing layer (i.e.,electrically insulating 106) of the nanochannel 105 have been lifted offto show the nanochannel 105. FIG. 3B shows the exposed portion 315 ofthe carbon nanotube 103 through the bottom location 310 of thenanochannel 105. This exposed portion 315 of the carbon nanotube 103touches and interacts with the single base 350 (which represents anyindividual base) of the target molecule 305 at a time. The exposedportion 315 of the carbon nanotube 103 may be 1 nm (nanometer), which isthe diameter d of the carbon nanotube 103. The width of the exposedportion 315 is the width of the nanochannel 105. The width ofnanochannel 105 can be 1 to 2 nm, which can help to linearize thesingle-stranded DNA. The 1 nm diameter of the carbon nanotube 103 of theexposed portion 315 only allows one base of the target molecule to touchthe exposed portion 315 at any time.

In FIG. 3B, the dashed lines show that the carbon nanotube 103 runsunderneath the electrically insulating material/film 104 and that thecarbon nanotube 103 electrically connects to the electrodes 107 and 108.Also, the dashed lines show that the carbon nanotube 103 is notelectrically connectable for interaction except at the exposed portion315.

FIGS. 4A and 4B are a method 400 for base recognition in an integrationof a transistor and a nanochannel system 200 according to an embodiment.Reference can be made to FIGS. 1-3 and 5.

A target molecule (e.g., the target molecule 305) is forced down to(touch) the carbon nanotube 103 a single base at a time in a nanochannel105 at block 405. The target molecule 305 is forced to the carbonnanotube 103 by applying a gate voltage (by voltage source 213) to thetop electrode 109 of the transistor, by a narrow thickness of thenanochannel 105, or both by applying the gate voltage to the topelectrode 109 of the transistor and by the narrow thickness of thenanochannel 105.

At block 410, the nanochannel 105 has been patterned over the carbonnanotube 103 to expose the exposed portion 315 of the carbon nanotube103 at a bottom wall of the carbon nanotube 103, and the top electrode109 of the transistor is positioned over the exposed portion 315 of thecarbon nanotube 103 up through nanochannel 105.

At block 415, the exposed portion 315 of the carbon nanotube 103 issmaller than a separating distance (e.g., distance X) between bases onthe target molecule 305, and the exposed portion 315 of the carbonnanotube 103 is configured (with a size) to only accommodate a singlebase (e.g., base 350) at a time.

The target molecule 305 is stretched by the narrow thickness of thenanochannel 105 and by applying a traverse voltage (by the voltagesource 211) across a length direction (e.g., from the inlet 210 to theoutlet 219) of the nanochannel 105 between a first electrode (e.g.,electrode 218) and a second electrode (e.g., electrode 219) at oppositeends of the nanochannel 105 in the length direction at block 420.

At block 425, the target molecule 305 is frictionally restricted by thenarrow thickness (and/or width) of the nanochannel 105 causing thetarget molecule to stretch as the target molecule 305 restrictedlytranslocates in the length direction while the traverse voltage isapplied.

A transistor current (when voltage of voltage source 213 is applied) ismeasured (by the ammeter 214) while the single base of the targetmolecule 305 is forced down to (touch) the exposed portion 315 of thecarbon nanotube 103 in the nanochannel 105, such that the single baseaffects the transistor current (e.g., causes the electrical current todrop or increase) at block 430.

At block 435, an identity (such as base A, G, C, and T) of the singlebase (e.g., base 350) is determined according to a change in thetransistor current while the single base is forced down to the exposedportion 315 of the carbon nanotube 103 in the nano channel 105.

Further, the method includes that when the target molecule is negativelycharged the gate voltage applied by the voltage source 215 is negative.When the target molecule is positively charged the gate voltage thevoltage source 215 is positive. Particularly, the gate voltage of thetop electrode (and to the body of the substrate 101) generates adownward force 207 through the nanochannel 105 above the exposed portion315, and the downward force 207 presses the target molecule down totouch (only) the exposed portion 315 of the carbon nanotube (while otherbases do not touch the exposed portion 315). When the single base isover the carbon nanotube 103, the downward force 207 presses the singlebase to touch the exposed portion 315 of the carbon nanotube 103 tosense the identity of the single base.

The target molecule 305 is deoxyribonucleic acid or ribonucleic acid.The nanochannel 105 is formed of an insulating material 104 except atthe exposed portion 315 of the carbon nanotube 103. Wherein thenanochannel 105 has a thickness (or depth) that is less than a thicknessof the insulating material 104 because the insulating material 104 isdeposited on both the carbon nanotube 103 and the insulating material102 layer underneath carbon nanotube.

The thickness (depth) of the nanochannel 105 is (substantially) between1 to 2 nanometers when the target molecule 305 is a singe strandpolynucleotide in order for the target molecule 305 to be stretched asit bumps/slides against the walls of the nanochannel 105. The thicknessof the nanochannel 105 is (substantially) between 2 to 4 nanometers whenthe target molecule 305 is a double strand polynucleotide in order forthe target molecule to be stretched.

Also, the thickness of the nanochannel 105 is determined by the diameterof the target molecule to be sequenced in order for the target moleculeto be frictionally restricted when translocating through the nanochannel105.

The traverse voltage (applied by the voltage source 211) issubstantially between 0 to 5 volts. The gate voltage (applied by thevoltage source 215) is substantially between −10 to 0 volts when thetarget molecule 305 is negatively charged. The gate voltage (applied bythe voltage source 215) is substantially between 0 to +10 volts when thetarget molecule is positively charged.

A coating molecule is applied to the carbon nanotube 103 (e.g., at leastat the exposed portion 315) to increase sensitivity of the transistor toaccept charges from the single base 350 being pressed to the exposedportion 315. The coating molecule increases a selectivity of bases ofthe target molecules which may cause certain bases to attach to theexposed portion 315. As one example, the coating molecule can be11-mercaptoundecanol, which can be switched based on the polarity by theexternal voltage (of the voltage source 213). The coating molecule canhelp to trap and sense the single base when the voltage is positive.

The transistor comprises a source electrode (e.g., electrode 107) and adrain electrode (e.g., electrode 108) connected by the carbon nanotube103, and wherein the transistor current flows from the source electrodeto the drain electrode through the carbon nanotube 103.

FIG. 5 illustrates an example of a computer 500 (e.g., as part of thecomputer test setup for testing and analysis) which may implement,control, and/or regulate the respective voltages of the voltage sources,respective measurements of the ammeters, and display screens fordisplaying various current amplitude (amplitude versus dwell (duration)time graphs for the applied voltage) as discussed herein. The computer500 also stores the respective electrical current amplitudes of eachbase tested and measured to be compared against the baselines currentamplitudes of different bases.

Various methods, procedures, modules, flow diagrams, tools,applications, circuits, elements, and techniques discussed herein mayalso incorporate and/or utilize the capabilities of the computer 500.Moreover, capabilities of the computer 500 may be utilized to implementfeatures of exemplary embodiments discussed herein. One or more of thecapabilities of the computer 500 may be utilized to implement, toconnect to, and/or to support any element discussed herein (asunderstood by one skilled in the art) in FIGS. 1-4. For example, thecomputer 500 which may be any type of computing device and/or testequipment (including ammeters, voltage sources, current meters,connectors, etc.). Input/output device 570 (having proper software andhardware) of computer 500 may include and/or be coupled to thenanodevices and structures discussed herein via cables, plugs, wires,electrodes, patch clamps, etc. Also, the communication interface of theinput/output devices 570 comprises hardware and software forcommunicating with, operatively connecting to, reading, and/orcontrolling voltage sources, ammeters, and current traces (e.g.,magnitude and time duration of current), etc., as discussed herein. Theuser interfaces of the input/output device 570 may include, e.g., atrack ball, mouse, pointing device, keyboard, touch screen, etc., forinteracting with the computer 500, such as inputting information, makingselections, independently controlling different voltages sources, and/ordisplaying, viewing and recording current traces for each base,molecule, biomolecules, etc.

Generally, in terms of hardware architecture, the computer 500 mayinclude one or more processors 510, computer readable storage memory520, and one or more input and/or output (I/O) devices 570 that arecommunicatively coupled via a local interface (not shown). The localinterface can be, for example but not limited to, one or more buses orother wired or wireless connections, as is known in the art. The localinterface may have additional elements, such as controllers, buffers(caches), drivers, repeaters, and receivers, to enable communications.Further, the local interface may include address, control, and/or dataconnections to enable appropriate communications among theaforementioned components.

The processor 510 is a hardware device for executing software that canbe stored in the memory 520. The processor 510 can be virtually anycustom made or commercially available processor, a central processingunit (CPU), a data signal processor (DSP), or an auxiliary processoramong several processors associated with the computer 500, and theprocessor 510 may be a semiconductor based microprocessor (in the formof a microchip) or a macroprocessor.

The computer readable memory 520 can include any one or combination ofvolatile memory elements (e.g., random access memory (RAM), such asdynamic random access memory (DRAM), static random access memory (SRAM),etc.) and nonvolatile memory elements (e.g., ROM, erasable programmableread only memory (EPROM), electronically erasable programmable read onlymemory (EEPROM), programmable read only memory (PROM), tape, compactdisc read only memory (CD-ROM), disk, diskette, cartridge, cassette orthe like, etc.). Moreover, the memory 520 may incorporate electronic,magnetic, optical, and/or other types of storage media. Note that thememory 520 can have a distributed architecture, where various componentsare situated remote from one another, but can be accessed by theprocessor 510.

The software in the computer readable memory 520 may include one or moreseparate programs, each of which comprises an ordered listing ofexecutable instructions for implementing logical functions. The softwarein the memory 520 includes a suitable operating system (O/S) 550,compiler 540, source code 530, and one or more applications 560 of theexemplary embodiments. As illustrated, the application 560 comprisesnumerous functional components for implementing the features, processes,methods, functions, and operations of the exemplary embodiments.

The operating system 550 may control the execution of other computerprograms, and provides scheduling, input-output control, file and datamanagement, memory management, and communication control and relatedservices.

The application 560 may be a source program, executable program (objectcode), script, or any other entity comprising a set of instructions tobe performed. When a source program, then the program is usuallytranslated via a compiler (such as the compiler 540), assembler,interpreter, or the like, which may or may not be included within thememory 520, so as to operate properly in connection with the O/S 550.Furthermore, the application 560 can be written as (a) an objectoriented programming language, which has classes of data and methods, or(b) a procedure programming language, which has routines, subroutines,and/or functions.

The I/O devices 570 may include input devices (or peripherals) such as,for example but not limited to, a mouse, keyboard, scanner, microphone,camera, etc. Furthermore, the I/O devices 570 may also include outputdevices (or peripherals), for example but not limited to, a printer,display, etc. Finally, the I/O devices 570 may further include devicesthat communicate both inputs and outputs, for instance but not limitedto, a NIC or modulator/demodulator (for accessing remote devices, otherfiles, devices, systems, or a network), a radio frequency (RF) or othertransceiver, a telephonic interface, a bridge, a router, etc. The I/Odevices 570 also include components for communicating over variousnetworks, such as the Internet or an intranet. The I/O devices 570 maybe connected to and/or communicate with the processor 510 utilizingBluetooth connections and cables (via, e.g., Universal Serial Bus (USB)ports, serial ports, parallel ports, FireWire, HDMI (High-DefinitionMultimedia Interface), etc.).

In exemplary embodiments, where the application 560 is implemented inhardware, the application 560 can be implemented with any one or acombination of the following technologies, which are each well known inthe art: a discrete logic circuit(s) having logic gates for implementinglogic functions upon data signals, an application specific integratedcircuit (ASIC) having appropriate combinational logic gates, aprogrammable gate array(s) (PGA), a field programmable gate array(FPGA), etc.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. It will be further understood that the terms “comprises”and/or “comprising,” when used in this specification, specify thepresence of stated features, integers, steps, operations, elements,and/or components, but do not preclude the presence or addition of onemore other features, integers, steps, operations, element components,and/or groups thereof.

The corresponding structures, materials, acts, and equivalents of allmeans or step plus function elements in the claims below are intended toinclude any structure, material, or act for performing the function incombination with other claimed elements as specifically claimed. Thedescription of the present invention has been presented for purposes ofillustration and description, but is not intended to be exhaustive orlimited to the invention in the form disclosed. Many modifications andvariations will be apparent to those of ordinary skill in the artwithout departing from the scope and spirit of the invention. Theembodiment was chosen and described in order to best explain theprinciples of the invention and the practical application, and to enableothers of ordinary skill in the art to understand the invention forvarious embodiments with various modifications as are suited to theparticular use contemplated

The flow diagrams depicted herein are just one example. There may bemany variations to this diagram or the steps (or operations) describedtherein without departing from the spirit of the invention. Forinstance, the steps may be performed in a differing order or steps maybe added, deleted or modified. All of these variations are considered apart of the claimed invention.

While the preferred embodiment to the invention had been described, itwill be understood that those skilled in the art, both now and in thefuture, may make various improvements and enhancements which fall withinthe scope of the claims which follow. These claims should be construedto maintain the proper protection for the invention first described.

What is claimed is:
 1. A method for base recognition in an integrationof a transistor and a nanochannel, the method comprising: forcing atarget molecule down to a carbon nanotube a single base at a time in thenanochannel, the target molecule being forced to the carbon nanotube byapplying a gate voltage to a top electrode of the transistor, by anarrow thickness of the nanochannel, or both by applying the gatevoltage to the top electrode of the transistor and by the narrowthickness of the nanochannel; wherein the nanochannel having beenpatterned over the carbon nanotube exposes an exposed portion of thecarbon nanotube at a bottom wall of the carbon nanotube, the topelectrode of the transistor positioned over the exposed portion of thecarbon nanotube through the nanochannel; wherein the exposed portion ofthe carbon nanotube is smaller than a separating distance between baseson the target molecule, the exposed portion of the carbon nanotube beingconfigured to only accommodate the single base at a time; stretching thetarget molecule by the narrow thickness of the nanochannel and byapplying a traverse voltage across a length direction of the nanochannelbetween a first electrode and a second electrode at opposite ends of thenanochannel in the length direction; wherein the target molecule isfrictionally restricted by the narrow thickness of the nanochannelcausing the target molecule to stretch as the target moleculerestrictedly translocates in the length direction while the traversevoltage is applied; measuring a transistor current while the single baseof the target molecule is forced down to the exposed portion of thecarbon nanotube in the nanochannel, the single base affecting thetransistor current; and determining an identity of the single baseaccording to a change in the transistor current while the single base isforced down to the exposed portion of the carbon nanotube in thenanochannel.
 2. The method of claim 1, wherein when the target moleculeis negatively charged the gate voltage is negative.
 3. The method ofclaim 1, wherein when the target molecule is positively charged the gatevoltage is positive.
 4. The method of claim 1, wherein the gate voltageof the top electrode generates a downward force through the nanochannelabove the exposed portion, the downward force pressing the targetmolecule down to touch the exposed portion of the carbon nanotube. 5.The method of claim 4, wherein when the single base is over the carbonnanotube, the downward force presses the single base to touch theexposed portion of the carbon nanotube to sense the identity of thesingle base.
 6. The method of claim 1, wherein the target molecule isdeoxyribonucleic acid or ribonucleic acid.
 7. The method of claim 1,wherein the nanochannel is formed of an insulating material except atthe exposed portion of the carbon nanotube.
 8. The method of claim 7,wherein the nanochannel has a thickness that is less than a thickness ofthe insulating material.
 9. The method of claim 1, wherein a thicknessof the nanochannel is substantially between 1 to 2 nanometers when thetarget molecule is a singe strand polynucleotide in order for the targetmolecule to be stretched.
 10. The method of claim 1, wherein a thicknessof the nanochannel is substantially between 2 to 4 nanometers when thetarget molecule is a double strand polynucleotide in order for thetarget molecule to be stretched.
 11. The method of claim 1, wherein athickness of the nanochannel is determined by a diameter of the targetmolecule to be sequenced in order for the target molecule to befrictionally restricted when translocating through the nanochannel. 12.The method of claim 1, wherein the traverse voltage is substantiallybetween 0 to 5 volts.
 13. The method of claim 1, wherein the gatevoltage is substantially between −10 to 0 volts when the target moleculeis negatively charged.
 14. The method of claim 1, wherein the gatevoltage is substantially between 0 to +10 volts when the target moleculeis positively charged.
 15. The method of claim 1, wherein a coatingmolecule is applied to the carbon nanotube to increase sensitivity ofthe transistor; wherein the coating molecule increases a selectivity ofbases of the target molecule.
 16. The method of claim 1, wherein thetransistor comprises a source electrode and a drain electrode connectedby the carbon nanotube; wherein the transistor current flows from thesource electrode to the drain electrode through the carbon nanotube.